Stabilizing effect of 5-nitroindole (universal base) on DNA duplexes immobilized on gel matrix

Effect of attachment of 1-(2-deoxy-beta D-ribofuranosyl)-5-nitroind (NIDR) to the ends of target sequence of oligonucleotides immobilized on gel micromatrix on stability of duplex formed by hybridization with DNA fragment was studied. It was shown that adjunction of NIDR to 5' as well as to 3' end results in increasing stability of duplexes although in the second case the extent of stabilization effect is essentially lower. Both 5' and 3' terminal NIDR exhibited no selectivity to the opposite base while the stabilizing effect depended dramatically on the nature of the adjacent base especially in the case of 5'-end-attached universal base. The neighborhood of purine bases decreased substantially the stabilizing effect of 5' terminal NIDR. In contrast with this, the stabilizing effect of 3' terminal NIDR was reduced only slightly by adjacent pyrimidine bases.